The role of ubiquinone in Caenorhabditis elegans longevity

Aging is an irreversible physiological process that affects all living organisms. Different mutations in the insulin signaling pathway and caloric restriction have been shown to retard aging in Caenorhabditis elegans. In addition, mutations or RNAi silencing of components of the respiratory chain results in the modification of adult life span. Another class of genes that affect life span in C. elegans is the clock (clk) genes. Particularly interesting is clk-1, which encodes an enzyme required for ubiquinone (coenzyme Q, CoQ) biosynthesis. Down-regulation by RNAi silencing of the genes required for ubiquinone biosynthesis also extends life span in C. elegans, and CoQ supplied in the diet also affects nematode longevity in both clk-1 and wild-type strains. Although there are many aspects that can be considered in aging, we focus this review on the role of CoQ in the longevity of C. elegans. We will review the current information about the biosynthesis of CoQ and its dietary supplementation related to the extension of life span. We will also analyze the function of CoQ in the electron transport chain and reactive oxygen species production in the context of aging. We hypothesize that the role of CoQ on longevity of C. elegans supports the oxidative damage theory of aging.     

Systematic analysis and prediction of longevity genes in Caenorhabditis elegans

An important task of aging research is to find genes that regulate lifespan. However, identification of genes related to longevity (referred to as longevity genes hereafter) through web-lab experiments such as genetic screens is a tedious and labor-intensive activity. Developing an algorithm to predict longevity genes should facilitate aging research. In this paper, we systematically analyzed properties of longevity genes in Caenorhabditis elegans and found that, when compared to genes not yet known to be involved in longevity, known longevity genes display the following features: (i) longer genomic sequences and protein sequences, (ii) a stronger tendency to co-express with other genes during a transition from dauer state (an extremely long lifespan) to non-dauer state (a normal lifespan), (iii) significant enrichment in certain functions and RNAi phenotypes, (iv) higher sequence conservation, and (v) higher in several network topological features such as degrees in a functional interaction network. Based on these features, we developed an algorithm to predict longevity genes in C. elegans and obtained 243 novel longevity genes with a precision rate of 0.85. Some of the predicted genes have been validated by published articles or wet lab experiments. The contribution of each feature to the predicted results was also evaluated.     

High-throughput gene mapping in Caenorhabditis elegans

Positional cloning of mutations in model genetic systems is a powerful method for the identification of targets of medical and agricultural importance. To facilitate the high-throughput mapping of mutations in Caenorhabditis elegans, we have identified a further 9602 putative new single nucleotide polymorphisms (SNPs) between two C. elegans strains, Bristol N2 and the Hawaiian mapping strain CB4856, by sequencing inserts from a CB4856 genomic DNA library and using an informatics pipeline to compare sequences with the canonical N2 genomic sequence. When combined with data from other laboratories, our marker set of 17,189 SNPs provides even coverage of the complete worm genome. To date, we have confirmed >1099 evenly spaced SNPs (one every 91 +/- 56 kb) across the six chromosomes and validated the utility of our SNP marker set and new fluorescence polarization-based genotyping methods for systematic and high-throughput identification of genes in C. elegans by cloning several proprietary genes. We illustrate our approach by recombination mapping and confirmation of the mutation in the cloned gene, dpy-18.     

New developmental insights from high-throughput biological analysis in Caenorhabditis elegans

The use of Caenorhabditis elegans as a model system for understanding animal development and human disease has long been recognized as an efficient tool of discovery. Recent developments, particularly in our understanding of RNA-mediated interference and its ability to modify gene activity, have facilitated the use of C. elegans in determining gene function via high-throughput analysis. These new strategies have provided a framework that allows investigators to analyse gene function globally at the genomic level and will likely become a prototypic model for biological analysis in the post-genome era.     

The Caenorhabditis elegans APC-related gene apr-1 is required for epithelial cell migration and Hox gene expression

Inactivation of the Caenorhabditis elegans APC-related gene (apr-1) has pointed at two separate functions of apr-1. First, apr-1 is required for the migration of epithelial cells during morphogenesis of the embryo. In this process, APR-1 may act in a Cadherin/alpha-Catenin/beta-Catenin complex as a component of adherens junctions. Second, apr-1 is required for Hox gene expression, most likely by positively regulating the activity of the Wingless signaling pathway. During embryogenesis, apr-1 is required for the expression of ceh-13 labial in anterior seam and muscle cells and during larval development, apr-1 is necessary for the expression of lin-39 deformed in the vulval precursor cells. Thus, APR-1 may positively regulate the activity of the beta-Catenin/Armadillo-related proteins HMP-2 in migrating epithelial cells and BAR-1 in the vulval precursor cells.     

The lin-14 locus of Caenorhabditis elegans controls the time of expression of specific postembryonic developmental events

The lin-14 locus of Caenorhabditis elegans plays an important role in specifying the normal timing and sequence of developmental events in the lateral hypodermal cell lineages. The results of gene dosage, complementation, and temperature-shift experiments indicate that the fates expressed by cells at successive stages of these cell lineages are specified by the level of lin-14 activity and that lin-14 acts at multiple times during development to control stage-specific choices of cell fate. Our observations suggest that during normal development a reduction in the level of lin-14 gene function causes the sequential expression of stage-specific cell fates.     

A method for the isolation of longevity mutants in the nematode Caenorhabditis elegans and initial results

The free-living nematode Caenorhabditis elegans is used as a genetically manipulable experimental system for the study of aging. Utilizing a temperature-sensitive sterile strain with a normal life span, a method is described for the isolation of mutant strains with significantly increased life spans. Eight mutant strains were isolated each having increased life spans. Two mutant strains were spontaneous dauer formers, accounting for their increased longevity. Another was chemotaxis-defective, causing reduced food intake which could account for its increased life span. Five mutants suffered from varying degrees of paralysis affecting their rate of pharyngeal pumping and food ingestion. The high correlation of the decreased rate of food ingestion of these mutants with their increased longevity is interpreted as indicating that the increased longevity is most likely due to reduced caloric intake. These results appear to indicate that specific life span genes are extremely rare or, alternatively, life span is controlled in a polygenic fashion.     

Cis‐regulatory mechanisms of gene expression in an olfactory neuron type in Caenorhabditis elegans

The generation of cellular diversity is dependent on the precise spatiotemporal regulation of gene expression by both cis‐ and trans‐acting mechanisms. The developmental principles regulating expression of specific gene subsets in individual cell types are not fully understood. Here we define the cis‐regulatory mechanisms driving expression of cell‐selective and broadly expressed genes in vivo in the AWB olfactory neuron subtype in C. elegans. We identify an element that is necessary to drive expression of neuron‐selective chemoreceptor genes in the AWB neurons, and show that this element functions in a context‐dependent manner. We find that the expression of broadly expressed sensory neuronal genes in the AWB neurons is regulated by diverse cis‐ and trans‐regulatory mechanisms that act partly in parallel to the pathways governing expression of AWB‐selective genes. We further demonstrate that cis‐acting mechanisms driving gene expression in the AWB neurons appear to have diverged in related nematode species. Our results provide insights into the cis‐regulatory logic driving cell‐specific gene expression, and suggest that variations in this logic contribute to the generation of functional diversity. Developmental Dynamics 238:3080–3092, 2009. © 2009 Wiley‐Liss, Inc.     

Comparison of collagen gene sequences in Ascaris suum and Caenorhabditis elegans

The nucleotide sequences of a 3060-bp fragment containing almost the entire coding sequence of one Ascaris suum collagen gene, and a 3019-bp pair fragment containing the 3' end of another A. suum collagen gene have been determined. The polypeptides encoded by these genes show a striking similarity to two Caenorhabditis elegans cuticular collagens, both in the position of the triple-helical regions and in the position of cysteine residues. The results of Northern blot hybridisation experiments together with dot blot analysis of RNA isolated from different adult worm tissues suggest that one of these genes is expressed in the adult nematode and that it encodes a protein of approximately 30 kDa.     

Immunity in Caenorhabditis elegans

Until very recently it was not known whether the invertebrate Caenorhabditis elegans was capable of mounting a specific immune response to protect itself from pathogens. It has only just become clear that this simple nematode in fact possesses a complex innate immune system, involving multiple signalling pathways and an armoury of antimicrobial proteins and peptides. Genetic and microarray approaches are now revealing the molecular cross-talk that exists between the different signalling cascades.     

Mutation in a mitochondrial ribosomal protein causes increased sensitivity to oxygen with decreased longevity in the nematode Caenorhabditis elegans

Oxygen is essential for animals, but high concentrations of oxygen are toxic to them probably because of an increase in reactive oxygen species (ROS). Many genes are involved in the reactions from which ROS are generated, but not much attention has been focused on them. To identify these genes, we screened for mutants with an altered sensitivity to oxidative stress in the nematode Caenorhabditis elegans and isolated a mutant, oxy‐5(qa5002). oxy‐5 showed an increased sensitivity to oxygen and decreased longevity. The decreased life span in oxy‐5 was probably due to increased oxidative stress because it was recovered to a normal level when oxy‐5 was cultured under hypoxic conditions. Our genetic analysis has revealed that the responsible gene for oxy‐5 encodes a protein similar to mitochondrial ribosomal protein S36. The OXY‐5 protein was highly expressed in the neurons, pharynx, and intestine, and expression of oxy‐5 from the pan‐neuronal H20 promoter efficiently suppressed the increased sensitivity to oxygen in oxy‐5. These findings suggested that oxy‐5 played an important role in the regulation of the sensitivity to oxygen in neuronal cells in C. elegans.     

Gene expression patterns associated with queen honey bee longevity

The oxidative stress theory of aging proposes that accumulation of oxidative damage is the main proximate cause of aging and that lifespan is determined by the rate at which this damage occurs. Two predictions from this theory are that long-lived organisms produce fewer ROS or have increased antioxidant production. Based in these predictions, molecular mechanisms to promote longevity could include either changes in the regulation of mitochondrial genes that affect ROS production or elevated expression of antioxidant genes. We explored these possibilities in the honey bee, a good model for the study of aging because it has a caste system in which the same genome produces both a long-lived queen and a short-lived worker. We measured mRNA levels for genes encoding eight of the most prominent antioxidant enzymes and five mitochondrial proteins involved in respiration. The expression of antioxidant genes generally decreased with age in queens, but not in workers. Expression of most mitochondrial genes, in particular CytC, was higher in young queens, but these genes showed a faster age-related decline relative to workers. One exception to this trend was COX-I in thorax. This resulted in higher COX-I/CytC ratios in old queens compared to old workers, which suggests caste-specific differences in mitochondrial function that might be related to the caste-specific differences in longevity. Queen honey bee longevity appears to have evolved via mechanisms other than increased antioxidant gene expression.     

Changes in gene expression associated with aging commonly originate during juvenile growth

In mammals, proliferation is rapid in many tissues during early postnatal life, causing rapid somatic growth. This robust proliferation is then suppressed as the animal approaches adult size, bringing many tissues to a quiescent state where proliferation occurs only as needed to replace dying cells. Recent evidence suggests that the mechanism responsible for this decline in proliferation involves a multi-organ genetic program. We hypothesized that this genetic program continues to progress into later adult life, eventually suppressing proliferation to levels below those needed for tissue renewal, thus contributing to aging. We therefore used expression microarray to compare the temporal changes in gene expression that occur in adult mouse organs during aging to those occurring as juvenile proliferation slows. We found that many of the changes in gene expression that occur during the aging process originate during the period of juvenile growth deceleration. Bioinformatic analyses of the genes that show persistent decline in expression throughout postnatal life indicated that cell-cycle-related genes are strongly over-represented. Thus, the findings support the hypothesis that the genetic program that slows juvenile growth to limit body size persists into adulthood and thus may eventually hamper tissue maintenance and repair, contributing to the aging process.     

Regulation of longevity by genes required for the functions of AIY interneuron in nematode Caenorhabditis elegans

In Caenorhabditis elegans, functional ttx-3, sra-11, ceh-10, and ceh-23 genes are required for the functions of AIY interneuron. Compared to wild-type N2, mutations in ttx-3 and ceh-10 significantly decreased lifespan, whereas mutations in sra-11 and ceh-23 did not obviously influence nematode lifespan. Mutations in ttx-3 and ceh-10 were associated closely with lower pumping rates at adult day 8 and caused a more rapid accumulated intestinal autofluorescence than wild-type N2. Mutations in ceh-10 remarkably affected fertility and egg number in the uterus. The regulation of ttx-3 and ceh-10 on longevity was not temperature-dependent, and ttx-3, and ceh-10 mutants all formed very few dauers at 27°C. The shortened lifespan of the ttx-3 or ceh-10 mutants was completely or largely rescued by expression of TTX-3 or CEH-10 in AIY interneurons. Moreover, the long-lived phenotype of the daf-2 mutant could be suppressed by both the ttx-3 and the ceh-10 mutations. Furthermore, ablation of AIY interneurons shortened the longevity of wild-type and the daf-2 mutant. Therefore, ttx-3 and ceh-10 regulate the longevity through influencing the insulin/IGF signaling pathway in C. elegans.